source: tags/release-1.1.8/src/Cubes/saveImage.cc

// -----------------------------------------------------------------------
// saveImage.cc: Write a wavelet-reconstructed or smoothed array to a
//               FITS file.
// -----------------------------------------------------------------------
// Copyright (C) 2006, Matthew Whiting, ATNF
//
// This program is free software; you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the
// Free Software Foundation; either version 2 of the License, or (at your
// option) any later version.
//
// Duchamp is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License
// along with Duchamp; if not, write to the Free Software Foundation,
// Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA
//
// Correspondence concerning Duchamp may be directed to:
//    Internet email: Matthew.Whiting [at] atnf.csiro.au
//    Postal address: Dr. Matthew Whiting
//                    Australia Telescope National Facility, CSIRO
//                    PO Box 76
//                    Epping NSW 1710
//                    AUSTRALIA
// -----------------------------------------------------------------------
#include <iostream>
#include <sstream>
#include <string>
#include <wcslib/wcs.h>
#include <wcslib/wcshdr.h>
#define WCSLIB_GETWCSTAB 
// define this so that we don't try and redefine wtbarr 
// (this is a problem when using cfitsio v.3 and g++ v.4)

#include <fitsio.h>
#include <duchamp/duchamp.hh>
#include <duchamp/Cubes/cubes.hh>
#include <duchamp/PixelMap/Voxel.hh>
#include <duchamp/PixelMap/Object3D.hh>

namespace duchamp
{

  /// @brief Write FITS headers in correct format for reconstructed array output 
  void writeReconHeaderInfo(fitsfile *fptr, Param &par, std::string nature);

  /// @brief Write FITS headers in correct format for smoothed array output 
  void writeSmoothHeaderInfo(fitsfile *fptr, Param &par);

  /// @brief Write FITS headers in correct format for mask array output 
  void writeMaskHeaderInfo(fitsfile *fptr, Param &par);
  //---------------------------------------------------------------------------

  void Cube::saveMaskCube()
  {
    /// @details
    ///  A function to save a mask to a FITS file, indicating where the
    ///  detections where made. The value of the detected pixels is
    ///  determined by the flagMaskWithObjectNum parameter: if true,
    ///  the value of the pixels is given by the corresponding object
    ///  ID number; if false, they take the value 1 for all
    ///  objects. Pixels not in a detected object have the value 0.

    int newbitpix = SHORT_IMG;
    long *fpixel = new long[this->numDim];
    for(int i=0;i<this->header().WCS().naxis;i++) fpixel[i]=1;
    int status = 0;  /* MUST initialize status */
    fitsfile *fptrOld, *fptrNew;         
    fits_open_file(&fptrOld,this->par.getImageFile().c_str(),READONLY,&status);
    if (status){
      duchampError("saveMask","Fits Error 1:");
      fits_report_error(stderr, status);
    }

    std::string fileout = "!" + this->par.outputMaskFile(); 
    // the ! is there so that it writes over an existing file.

    status = 0;
    fits_create_file(&fptrNew,fileout.c_str(),&status);
    if (status){
      duchampError("saveMask","Fits Error 2:");
      fits_report_error(stderr, status);
    }
    else {
      status = 0;
      fits_movabs_hdu(fptrOld, 1, NULL, &status);
      if (status){
        duchampError("saveMask","Fits Error 3:");
        fits_report_error(stderr, status);
      }
      status = 0;
      fits_copy_header(fptrOld, fptrNew, &status);
      if (status){
        duchampError("saveMask","Fits Error 4:");
        fits_report_error(stderr, status);
      }
      status = 0;
      fits_update_key(fptrNew, TINT, "BITPIX", &newbitpix, 
                      "number of bits per data pixel", &status);
      if (status){
        duchampError("saveMask","Fits Error 5:");
        fits_report_error(stderr, status);
      }
      float bscale=1., bzero=0.;
      fits_update_key(fptrNew, TFLOAT, "BSCALE", &bscale, "", &status);
      fits_update_key(fptrNew, TFLOAT, "BZERO", &bzero, "", &status);
      fits_set_bscale(fptrNew, 1, 0, &status);
      if (status){
        duchampError("saveMask","Fits Error 6:");
        fits_report_error(stderr, status);
      }
      std::string newunits;
      if(this->par.getFlagMaskWithObjectNum())
        newunits = "Object ID";
      else
        newunits = "Detection flag";
      fits_update_key(fptrNew, TSTRING, "BUNIT", (char *)newunits.c_str(), "", &status);
      if (status){
        duchampError("saveMask","Fits Error 7:");
        fits_report_error(stderr, status);
      }
      char *comment = new char[80];
      long dud;
      // Need to correct the dimensions, if we have subsectioned the image
      if(this->par.getFlagSubsection()){
        std::stringstream naxis;
        fits_read_key(fptrOld, TLONG, (char *)naxis.str().c_str(), &dud, comment, &status);
        fits_update_key(fptrNew, TLONG, (char *)naxis.str().c_str(),
                        &(this->axisDim[0]), comment, &status);
        naxis.str("");
        naxis << "NAXIS" << this->head.WCS().lat;
        fits_read_key(fptrOld, TLONG, (char *)naxis.str().c_str(), &dud, comment, &status);
        fits_update_key(fptrNew, TLONG, (char *)naxis.str().c_str(), 
                        &(this->axisDim[1]), comment, &status);
        naxis.str("");
        naxis << "NAXIS" << this->head.WCS().spec;
        fits_read_key(fptrOld, TLONG, (char *)naxis.str().c_str(), &dud, comment, &status);
        fits_update_key(fptrNew, TLONG, (char *)naxis.str().c_str(), 
                        &(this->axisDim[2]), comment, &status);
      }

      delete [] comment;

      writeMaskHeaderInfo(fptrNew, this->par);
        
      short *mask = new short[this->numPixels];
      for(int i=0;i<this->numPixels;i++) mask[i]=0;
      for(unsigned int o=0;o<this->objectList->size();o++){
        std::vector<PixelInfo::Voxel> voxlist = 
          this->objectList->at(o).pixels().getPixelSet();
        for(unsigned int p=0;p<voxlist.size();p++){
          int pixelpos = voxlist[p].getX() + this->axisDim[0]*voxlist[p].getY() + 
            this->axisDim[0]*this->axisDim[1]*voxlist[p].getZ();
          if(this->par.getFlagMaskWithObjectNum()) mask[pixelpos] = this->objectList->at(o).getID();
          else mask[pixelpos] = 1;
        }
      }
      status=0;
      fits_write_pix(fptrNew, TSHORT, fpixel, this->numPixels, mask, &status);
      if(status){
        duchampError("saveMask","Fits Error 8:");
        fits_report_error(stderr,status);
      }
      status = 0;
      fits_close_file(fptrNew, &status);
      if (status){
        duchampError("saveMask","Fits Error 9:");
        fits_report_error(stderr, status);
      }

      delete [] mask;

    }

    delete [] fpixel;

  }
  
  //---------------------------------------------------------------------------

  void Cube::saveSmoothedCube()
  {
    /// @brief
    ///   A function to save the smoothed arrays to a FITS file.
    ///   Additional header keywords are written as well, indicating the
    ///   width of the Hanning filter or the dimensions of the Gaussian
    ///   kernel.
    ///   The file is always written -- if the filename (as calculated 
    ///    based on the parameters) exists, then it is overwritten.
  
    float blankval = this->par.getBlankPixVal();

    int status = 0;  /* MUST initialize status */
    fitsfile *fptrOld, *fptrNew;         
    fits_open_file(&fptrOld,this->par.getFullImageFile().c_str(),READONLY,&status);
    if (status) fits_report_error(stderr, status);
  
    if(this->par.getFlagOutputSmooth()){
      std::string fileout = "!" + this->par.outputSmoothFile(); 
      // the ! is there so that it writes over an existing file.

      status = 0;
      fits_create_file(&fptrNew,fileout.c_str(),&status);
      if (status)
        fits_report_error(stderr, status);
      else {
        status = 0;
        fits_movabs_hdu(fptrOld, 1, NULL, &status);
        if (status) fits_report_error(stderr, status);
        status = 0;
        fits_copy_header(fptrOld, fptrNew, &status);
        if (status) fits_report_error(stderr, status);

        writeSmoothHeaderInfo(fptrNew, this->par);

        if(this->par.getFlagBlankPix())
          fits_write_imgnull(fptrNew, TFLOAT, 1, this->numPixels, this->recon, &blankval, &status);
        else 
          fits_write_img(fptrNew, TFLOAT, 1, this->numPixels, this->recon, &status);

        status = 0;
        fits_close_file(fptrNew, &status);
        if (status) fits_report_error(stderr, status);

      }
    }

  }

  //---------------------------------------------------------------------------

  void Cube::saveReconstructedCube()
  {
    /// @details
    ///  A function to save the reconstructed and/or residual arrays.
    ///   A number of header keywords are written as well, indicating the 
    ///    nature of the reconstruction that has been done.
    ///   The file is always written -- if the filename (as calculated 
    ///    based on the recon parameters) exists, then it is overwritten.
  
    float blankval = this->par.getBlankPixVal();

    int status = 0;  /* MUST initialize status */
    fitsfile *fptrOld, *fptrNew;         
    fits_open_file(&fptrOld,this->par.getFullImageFile().c_str(),READONLY,&status);
    if (status) fits_report_error(stderr, status);
  
    if(this->par.getFlagOutputRecon()){
      std::string fileout = "!" + this->par.outputReconFile(); 
      // the ! is there so that it writes over an existing file.

      status = 0;
      fits_create_file(&fptrNew,fileout.c_str(),&status);
      if (status)
        fits_report_error(stderr, status);
      else
        {
          status = 0;
          fits_movabs_hdu(fptrOld, 1, NULL, &status);
          if (status) fits_report_error(stderr, status);
          status = 0;
          fits_copy_header(fptrOld, fptrNew, &status);
          if (status) fits_report_error(stderr, status);

          writeReconHeaderInfo(fptrNew, this->par, "recon");

          if(this->par.getFlagBlankPix())
            fits_write_imgnull(fptrNew, TFLOAT, 1, this->numPixels, this->recon, &blankval, &status);
          else  
            fits_write_img(fptrNew, TFLOAT, 1, this->numPixels, this->recon, &status);

          status = 0;
          fits_close_file(fptrNew, &status);
          if (status) fits_report_error(stderr, status);
        }
    }


    if(this->par.getFlagOutputResid()){
      float *resid = new float[this->numPixels];
      for(int i=0;i<this->numPixels;i++) 
        resid[i] = this->array[i] - this->recon[i];

      std::string fileout = "!" + this->par.outputResidFile(); 
      // the ! is there so that it writes over an existing file.
      status = 0;
      fits_create_file(&fptrNew,fileout.c_str(),&status);
      if (status)
        fits_report_error(stderr, status);
      else
        {
          status = 0;
          fits_movabs_hdu(fptrOld, 1, NULL, &status);
          if (status) fits_report_error(stderr, status);
          status = 0;
          fits_copy_header(fptrOld, fptrNew, &status);
          if (status) fits_report_error(stderr, status);

          writeReconHeaderInfo(fptrNew, this->par, "resid");

          if(this->par.getFlagBlankPix())
            fits_write_imgnull(fptrNew, TFLOAT, 1, this->numPixels, resid, &blankval, &status);
          else  
            fits_write_img(fptrNew, TFLOAT, 1, this->numPixels, resid, &status);

          fits_close_file(fptrNew, &status);
        }
      delete [] resid;
    }


  }

  //---------------------------------------------------------------------------

  void writeReconHeaderInfo(fitsfile *fptr, Param &par, std::string nature)
  {
    /// @details
    ///   A simple function that writes all the necessary keywords and comments
    ///    to the FITS header pointed to by fptr.
    ///   The keyword names and comments are taken from duchamp.hh
    ///   The parameter "nature" indicates what type of file is being written:
    ///    should be either "recon" or "resid".

    int status = 0;
    std::string explanation = "",ReconResid="";

    fits_write_history(fptr, (char *)header_reconHistory1.c_str(), &status);
                                   
    fits_write_history(fptr, (char *)header_reconHistory2.c_str(), &status);

    fits_write_history(fptr, (char *)header_reconHistory_input.c_str(), &status);

    fits_write_history(fptr, (char *)par.getImageFile().c_str(), &status);

    if(par.getFlagSubsection()){
      fits_write_comment(fptr,(char *)header_reconSubsection_comment.c_str(),
                         &status);
      fits_write_key(fptr, TSTRING, (char *)keyword_subsection.c_str(), 
                     (char *)par.getSubsection().c_str(),
                     (char *)comment_subsection.c_str(), &status);
    }
    
    fits_write_comment(fptr, (char *)header_atrous_comment.c_str(), &status);

    float valf = par.getAtrousCut();
    fits_write_key(fptr, TFLOAT, (char *)keyword_snrRecon.c_str(), &valf, 
                   (char *)comment_snrRecon.c_str(), &status);

    int vali = par.getReconDim();
    fits_write_key(fptr, TINT, (char *)keyword_reconDim.c_str(), &vali, 
                   (char *)comment_reconDim.c_str(), &status);

    vali = par.getMinScale();
    fits_write_key(fptr, TINT, (char *)keyword_scaleMin.c_str(), &vali, 
                   (char *)comment_scaleMin.c_str(), &status);

    vali = par.getFilterCode();
    fits_write_key(fptr, TINT, (char *)keyword_filterCode.c_str(), &vali, 
                   (char *)comment_filterCode.c_str(), &status);

    if(nature == "recon"){
      explanation = "Duchamp: This is the RECONSTRUCTED cube";
      ReconResid = "RECON";
    }
    else if(nature == "resid"){
      explanation = "Duchamp: This is the RESIDUAL cube";
      ReconResid = "RESID";
    }
    else duchampWarning("write_header_info","explanation not present!\n");
    fits_write_comment(fptr, (char *)explanation.c_str(), &status);
    fits_write_key(fptr, TSTRING, (char *)keyword_ReconResid.c_str(), 
                   (char *)ReconResid.c_str(), 
                   (char *)comment_ReconResid.c_str(), &status);

  }

  //---------------------------------------------------------------------------

  void writeSmoothHeaderInfo(fitsfile *fptr, Param &par)
  {
    /// @details
    ///   A simple function that writes all the necessary keywords and comments
    ///    to the FITS header pointed to by fptr.
    ///   The keyword names and comments are taken from duchamp.hh

    int status = 0;

    fits_write_history(fptr, (char *)header_smoothHistory.c_str(), &status);
    status = 0;
    fits_write_history(fptr, (char *)header_smoothHistory_input.c_str(),&status);
    status = 0;
    fits_write_history(fptr, (char *)par.getImageFile().c_str(), &status);

    if(par.getFlagSubsection()){
      status = 0;
      fits_write_comment(fptr,(char *)header_smoothSubsection_comment.c_str(),
                         &status);
      status = 0;
      fits_write_key(fptr, TSTRING, (char *)keyword_subsection.c_str(), 
                     (char *)par.getSubsection().c_str(),
                     (char *)comment_subsection.c_str(), &status);
    }
    
    if(par.getSmoothType()=="spatial"){
      // if kernMin is negative (not defined), make it equal to kernMaj
      if(par.getKernMin() < 0) par.setKernMin(par.getKernMaj());

      fits_write_key(fptr, TSTRING, (char *)keyword_smoothtype.c_str(),
                     (char *)header_smoothSpatial.c_str(),
                     (char *)comment_smoothtype.c_str(), &status);
      float valf = par.getKernMaj();
      fits_write_key(fptr, TFLOAT, (char *)keyword_kernmaj.c_str(), &valf,
                     (char *)comment_kernmaj.c_str(), &status);
      valf = par.getKernMin();
      fits_write_key(fptr, TFLOAT, (char *)keyword_kernmin.c_str(), &valf,
                     (char *)comment_kernmin.c_str(), &status);
      valf = par.getKernPA();
      fits_write_key(fptr, TFLOAT, (char *)keyword_kernpa.c_str(), &valf,
                     (char *)comment_kernpa.c_str(), &status);
    }
    else if(par.getSmoothType()=="spectral"){
      fits_write_key(fptr, TSTRING, (char *)keyword_smoothtype.c_str(),
                     (char *)header_smoothSpectral.c_str(),
                     (char *)comment_smoothtype.c_str(), &status);
      int vali = par.getHanningWidth();
      fits_write_key(fptr, TINT, (char *)keyword_hanningwidth.c_str(), &vali,
                     (char *)comment_hanningwidth.c_str(), &status);
    }
  }

  //---------------------------------------------------------------------------

  void writeMaskHeaderInfo(fitsfile *fptr, Param &par)
  {
    /// @details
    ///   A simple function that writes all the necessary keywords and comments
    ///    to the FITS header pointed to by fptr.
    ///   The keyword names and comments are taken from duchamp.hh

    int status = 0;

    fits_write_history(fptr, (char *)header_maskHistory.c_str(), &status);
    status = 0;
    fits_write_history(fptr, (char *)header_maskHistory_input.c_str(),&status);
    status = 0;
    fits_write_history(fptr, (char *)par.getImageFile().c_str(), &status);

    if(par.getFlagSubsection()){
      status = 0;
      fits_write_comment(fptr,(char *)header_maskSubsection_comment.c_str(),
                         &status);
      status = 0;
      fits_write_key(fptr, TSTRING, (char *)keyword_subsection.c_str(), 
                     (char *)par.getSubsection().c_str(),
                     (char *)comment_subsection.c_str(), &status);
    }
  }

}